title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1329 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: An enigmatic decoupling between heat stress and coral bleaching on the Great Barrier Reef link: https://peerj.com/articles/7473 last-modified: 2019-08-12 description: Ocean warming threatens the functioning of coral reef ecosystems by inducing mass coral bleaching and mortality events. The link between temperature and coral bleaching is now well-established based on observations that mass bleaching events usually occur when seawater temperatures are anomalously high. However, times of high heat stress but without coral bleaching are equally important because they can inform an understanding of factors that regulate temperature-induced bleaching. Here, we investigate the absence of mass coral bleaching on the Great Barrier Reef (GBR) during austral summer 2004. Using four gridded sea surface temperature data products, validated with in situ temperature loggers, we demonstrate that the summer of 2004 was among the warmest summers of the satellite era (1982–2017) on the GBR. At least half of the GBR experienced temperatures that were high enough to initiate bleaching in other years, yet mass bleaching was not reported during 2004. The absence of bleaching is not fully explained by wind speed or cloud cover. Rather, 2004 is clearly differentiated from bleaching years by the slow speed of the East Australian Current (EAC) offshore of the GBR. An anomalously slow EAC during summer 2004 may have dampened the upwelling of nutrient-rich waters onto the GBR shelf, potentially mitigating bleaching due to the lower susceptibility of corals to heat stress in low-nutrient conditions. Although other factors such as irradiance or acclimatization may have played a role in the absence of mass bleaching, 2004 remains a key case study for demonstrating the dynamic nature of coral responses to marine heatwaves. creator: Thomas M. DeCarlo creator: Hugo B. Harrison uri: https://doi.org/10.7717/peerj.7473 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 DeCarlo and Harrison title: Efficient virus-induced gene silencing in Hibiscus hamabo Sieb. et Zucc. using tobacco rattle virus link: https://peerj.com/articles/7505 last-modified: 2019-08-12 description: BackgroundHibiscus hamabo Sieb. et Zucc. is a semi-mangrove plant used for the ecological restoration of saline-alkali land, coastal afforestation and urban landscaping. The genetic transformation H. hamabo is currently inefficient and laborious, restricting gene functional studies on this species. In plants, virus-induced gene silencing provides a pathway to rapidly and effectively create targeted gene knockouts for gene functional studies.MethodsIn this study, we tested the efficiency of a tobacco rattle virus vector in silencing the cloroplastos alterados 1 (CLA1) gene through agroinfiltration.ResultsThe leaves of H. hamabo showed white streaks typical of CLA1 gene silencing three weeks after agroinfiltration. In agroinfiltrated H. hamabo plants, the CLA1 expression levels in leaves with white streaks were all significantly lower than those in leaves from mock-infected and control plants.ConclusionsThe system presented here can efficiently silence genes in H. hamabo and may be a powerful tool for large-scale reverse-genetic analyses of gene functions in H. hamabo. creator: Zhiquan Wang creator: Xiaoyang Xu creator: Longjie Ni creator: Jinbo Guo creator: Chunsun Gu uri: https://doi.org/10.7717/peerj.7505 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Wang et al. title: Transplantation of adipose-derived stem cells overexpressing inducible nitric oxide synthase ameliorates diabetes mellitus-induced erectile dysfunction in rats link: https://peerj.com/articles/7507 last-modified: 2019-08-12 description: BackgroundErectile dysfunction is a major complication of diabetes mellitus. Adipose-derived stem cells (ADSCs) have attracted much attention as a promising tool for the treatment of diabetes mellitus-induced erectile dysfunction (DMED). Inducible nitric oxide synthase (iNOS) plays an important role in protecting penile tissues from fibrosis. The aim of this study was to determine the efficacy of ADSCs overexpressing iNOS on DMED in rats.MethodsADSCs were isolated and infected with adenovirus overexpressing iNOS (named as ADSCs-iNOS). The expression of iNOS was detected using western blot analysis and real-time PCR. Rats were randomly assigned into five groups: control group, DMED group, ADSCs group, ADSCs-EGFP group and ADSCs-iNOS group. 5 × 105 cells were given once via the intracorporal route. Two weeks after treatment, erectile function was assessed by electrical stimulation of the cavernous nerve. Penile tissues were obtained and evaluated at histology level.ResultsWe found that ADSCs-iNOS had significantly higher expression of iNOS at mRNA and protein levels and generated more nitric oxide (NO). ADSCs-iNOS reduced collagen I and collagen IV expression of corpus cavernosum smooth muscle cells (CCSMCs) in cell co-culture model. Transforming growth factor-β1 expression in CCSMCs reduced following co-culture with ADSCs-iNOS. Injection of ADSCs-iNOS significantly ameliorated DMED in rats and decreased collagen/smooth muscle cell ratio of penile tissues. Moreover, elevated NO and cyclic guanosine monophosphate concentrations were detected in penile tissues of ADSCs-iNOS group.ConclusionTaken together, ADSCs-iNOS significantly improved erectile function of DMED rats. The therapeutic effect may be achieved by increased NO generation and the suppression of collagen I and collagen IV expression in the CCSMCs to decrease penile fibrosis. creator: Yan Zhang creator: Jun Yang creator: Li Zhuan creator: Guanghui Zang creator: Tao Wang creator: Jihong Liu uri: https://doi.org/10.7717/peerj.7507 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Zhang et al. title: The effects of high versus low talker variability and individual aptitude on phonetic training of Mandarin lexical tones link: https://peerj.com/articles/7191 last-modified: 2019-08-09 description: High variability (HV) training has been found to be more effective than low variability (LV) training when learning various non-native phonetic contrasts. However, little research has considered whether this applies to the learning of tone contrasts. The only two relevant studies suggested that the effect of HV training depends on the perceptual aptitude of participants (Perrachione et al., 2011; Sadakata & McQueen, 2014). The present study extends these findings by examining the interaction between individual aptitude and input variability using natural, meaningful second language input (both previous studies used pseudowords). A total of 60 English speakers took part in an eight session phonetic training paradigm. They were assigned to high/low/high-blocked variability training groups and learned real Mandarin tones and words. Individual aptitude was measured following previous work. Learning was measured using one discrimination task, one identification task and two production tasks. All tasks assessed generalization. All groups improved in both the production and perception of tones which transferred to untrained voices and items, demonstrating the effectiveness of training despite the increased complexity compared with previous research. Although the LV group exhibited an advantage with the training stimuli, there was no evidence for a benefit of high-variability in any of the tests of generalisation. Moreover, although aptitude significantly predicted performance in discrimination, identification and training tasks, no interaction between individual aptitude and variability was revealed. Additional Bayes Factor analyses indicated substantial evidence for the null for the hypotheses of a benefit of high-variability in generalisation, however the evidence regarding the interaction was ambiguous. We discuss these results in light of previous findings. creator: Hanyu Dong creator: Meghan Clayards creator: Helen Brown creator: Elizabeth Wonnacott uri: https://doi.org/10.7717/peerj.7191 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Dong et al. title: Taxonomic revision of the genus Cranichis (Orchidaceae, Cranichideae) in Colombia link: https://peerj.com/articles/7385 last-modified: 2019-08-09 description: The geographical range of the orchid genus Cranichis extends from USA, Central America, and the Caribbean to Bolivia and Argentina—with the greatest diversity observed in the Andean region. This taxon embraces herbs with the scape and basal leaves developing from a single, terminal bud and having the scape enclosed in several sheaths. The small, non-resupinate, flowers are arranged in a racemose inflorescence. The petals and lip are free from the column part and their gynostemium is short and massive. In this paper, the synopsis of Cranichis in Colombia is presented. Each species occurring in the country is characterized and illustrated. The information about habitat and distribution of national genus representatives are provided. Several groups of species that are very similar in their morphology are delineated to facilitate process of species identification. A total of 10 species are described here as new. Lectotypes for the six species Cranichis ciliata, C. fendleri, C. mandonii, C. tenuis, C. viereckii, and C. wageneri have been selected. Additionally, two new nomenclatorial combinations within Ocampoa are proposed. creator: Dariusz L. Szlachetko creator: Marta Kolanowska uri: https://doi.org/10.7717/peerj.7385 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Szlachetko and Kolanowska title: Functional group based marine ecosystem assessment for the Bay of Biscay via elasticity analysis link: https://peerj.com/articles/7422 last-modified: 2019-08-09 description: The transitory and long-term elasticities of the Bay of Biscay ecosystem to density-independent and density-dependent influences were estimated within a state space model that accounted for both process and observation uncertainties. A functional group based model for the Bay of Biscay fish ecosystem was fit to time series obtained from scientific survey and commercial catch and effort data. The observation model parameters correspond to the unknown catchabilities and observation error variances that vary across the commercial fisheries and fishery-independent scientific surveys. The process model used a Gompertz form of density dependence, which is commonly used for the analysis of multivariate ecological time series, with unknown time-varying fishing mortalities. Elasticity analysis showed that the process model parameters are directly interpretable in terms of one-year look-ahead prediction elasticities, which measure the proportional response of a functional group in the next year given a proportional change to a variable or parameter in the current year. The density dependent parameters were also shown to define the elasticities of the long term means or quantiles of the functional groups to changes in fishing pressure. Evidence for the importance of indirect effects, mediated by density dependence, in determining the ecosystem response of the Bay of Biscay to changes in fishing pressure is presented. The state space model performed favourably in an assessment of model adequacy that compared observations of catch per unit effort against cross-validation predictive densities blocked by year. creator: Geoffrey R. Hosack creator: Verena M. Trenkel uri: https://doi.org/10.7717/peerj.7422 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Hosack and Trenkel title: Potential benefits from global warming to the thermal biology and locomotor performance of an endangered Patagonian lizard link: https://peerj.com/articles/7437 last-modified: 2019-08-09 description: Global warming can significantly affect many aspects of the biology of animal species, including their thermal physiology and physiological performance. Thermal performance curves provide a heuristic model to evaluate the impacts of temperature on the ecophysiology of ectotherms. When integrated with other thermal biology parameters, they can be used to predict the impacts of climate change on individual fitness and population viability. In this study, we combine holistic measures of thermal physiology and the thermal sensitivity of locomotor performance with environmental temperatures measured at fine scale to estimate the vulnerability to global warming of the endangered Patagonian lizard Phymaturus tenebrosus. Our results indicate that this lizard exhibits its preferred temperatures and maximum locomotor performance at higher temperatures than the mean temperature it currently experiences in its habitat. In addition, it exhibits a low effectiveness of thermoregulation, being a poor thermoregulator. In view of the results obtained, we suggest that the climatic conditions of Patagonia may be advantageous for P. tenebrosus to survive future global warming, since its thermal physiology and locomotor performance may improve under increasing in environmental temperatures in its habitat. creator: Facundo Cabezas-Cartes creator: Jimena B. Fernández creator: Fernando Duran creator: Erika L. Kubisch uri: https://doi.org/10.7717/peerj.7437 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2019 Cabezas-Cartes et al. title: Horse phenotyping based on video image analysis of jumping performance for conservation breeding link: https://peerj.com/articles/7450 last-modified: 2019-08-09 description: BackgroundMany horse breeds in the world are reserved as genetic resources; however, their characteristics seem to be insufficiently clarified, especially in terms of horse performance. Two jumping ability evaluation methods have been used to compare different types of performance breeds and on this basis their applicability for precision phenotyping has been determined.MethodsJumping data of 186 young Polish Warmblood stallions (27 with an endangered status) bred for sport and multipurpose use was collected during their performance tests organised under identical environmental conditions following the same guidelines. Jumping data consisted of objective measurements of free jumping parameters and the marks for jumping. Video recordings of 514 jumps (73 records for 27 stallions with an endangered status) were collected using a digital Panasonic AG-EZ 35 camera (25 fr/sec). Filming was recorded during a free jumping test in the line on a doublebarre obstacle (100–120 cm × 100 cm). Spatial and temporal variables of the jump were measured. The analysis of variance was performed (SAS, General Linear Model and Mixed procedures) using the statistical model, which included the random effect of the horse and fixed effects of the year of test, breeding status, height of jump and the successive number of the jump for objective kinematic data. The fixed effects of the year of test and breeding status were included in the model for subjective performance test data.ResultsPerformance marks for free jumping were lower in the endangered group of stallions in the trainers’ opinion (p ≤ 0.05), while no statistically significant differences were found in the judges’ opinions. Statistically significant differences in jumping variables were measured for the bascule points—the elevations of the withers and croup were higher in the endangered group (p ≤ 0.001) and the take-off time was prolonged (p ≤ 0.05), which explained the subjective evaluation.DiscussionThe use of objective evaluation methods provides important information for practice, as phenotypic differences between horses may be unclear in the subjective evaluation. The objective evaluation should be used to characterise the performance potential of different breeds, because the information from the evaluators might not be consistent. Such characteristics should be recorded at least for every new population. creator: Dorota Lewczuk creator: Ewa Metera-Zarzycka uri: https://doi.org/10.7717/peerj.7450 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Lewczuk and Metera-Zarzycka title: Musculoskeletal models of a human and bonobo finger: parameter identification and comparison to in vitro experiments link: https://peerj.com/articles/7470 last-modified: 2019-08-09 description: IntroductionKnowledge of internal finger loading during human and non-human primate activities such as tool use or knuckle-walking has become increasingly important to reconstruct the behaviour of fossil hominins based on bone morphology. Musculoskeletal models have proven useful for predicting these internal loads during human activities, but load predictions for non-human primate activities are missing due to a lack of suitable finger models. The main goal of this study was to implement both a human and a representative non-human primate finger model to facilitate comparative studies on metacarpal bone loading. To ensure that the model predictions are sufficiently accurate, the specific goals were: (1) to identify species-specific model parameters based on in vitro measured fingertip forces resulting from single tendon loading and (2) to evaluate the model accuracy of predicted fingertip forces and net metacarpal bone loading in a different loading scenario.Materials & MethodsThree human and one bonobo (Pan paniscus) fingers were tested in vitro using a previously developed experimental setup. The cadaveric fingers were positioned in four static postures and load was applied by attaching weights to the tendons of the finger muscles. For parameter identification, fingertip forces were measured by loading each tendon individually in each posture. For the evaluation of model accuracy, the extrinsic flexor muscles were loaded simultaneously and both the fingertip force and net metacarpal bone force were measured. The finger models were implemented using custom Python scripts. Initial parameters were taken from literature for the human model and own dissection data for the bonobo model. Optimized model parameters were identified by minimizing the error between predicted and experimentally measured fingertip forces. Fingertip forces and net metacarpal bone loading in the combined loading scenario were predicted using the optimized models and the remaining error with respect to the experimental data was evaluated.ResultsThe parameter identification procedure led to minor model adjustments but considerably reduced the error in the predicted fingertip forces (root mean square error reduced from 0.53/0.69 N to 0.11/0.20 N for the human/bonobo model). Both models remained physiologically plausible after the parameter identification. In the combined loading scenario, fingertip and net metacarpal forces were predicted with average directional errors below 6° and magnitude errors below 12%.ConclusionsThis study presents the first attempt to implement both a human and non-human primate finger model for comparative palaeoanthropological studies. The good agreement between predicted and experimental forces involving the action of extrinsic flexors—which are most relevant for forceful grasping—shows that the models are likely sufficiently accurate for comparisons of internal loads occurring during human and non-human primate manual activities. creator: Alexander Synek creator: Szu-Ching Lu creator: Evie E. Vereecke creator: Sandra Nauwelaerts creator: Tracy L. Kivell creator: Dieter H. Pahr uri: https://doi.org/10.7717/peerj.7470 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Synek et al. title: Test-retest reliability of a smartphone app for measuring core stability for two dynamic exercises link: https://peerj.com/articles/7485 last-modified: 2019-08-09 description: BackgroundRecently, there has been growing interest in using smartphone applications to assess gait speed and quantify isometric core stability exercise intensity. The purpose of this study was to investigate the between-session reliability and minimal detectable change of a smartphone app for two dynamic exercise tests of the lumbopelvic complex.MethodsThirty-three healthy young and active students (age: 22.3 ± 5.9 years, body weight: 66.9 ± 11.3 kg, height: 167.8 ± 10.3 cm) participated in this study. Intraclass correlation coefficient (ICC), coefficient of variation (%CV), and Bland–Altman plots were used to verify the reliability of the test. The standard error of measurement (SEM) and the minimum detectable difference (MDD) were calculated for clinical applicability.ResultsThe ICCs ranged from 0.73 to 0.96, with low variation (0.9% to 4.8%) between days of assessments. The Bland–Altman plots and one-sample t-tests (p > 0.05) indicated that no dynamic exercise tests changed systematically. Our analyses showed that SEM 0.6 to 1.5 mm/s-2) and MDD (2.1 to 3.5 mm/s-2).ConclusionThe OCTOcore app is a reliable tool to assess core stability for two dynamic exercises. A minimal change of 3.5 mm/s-2 is needed to be confident that the change is not a measurement error between two sessions. creator: Paloma Guillén-Rogel creator: Cristina Franco-Escudero creator: Pedro J. Marín uri: https://doi.org/10.7717/peerj.7485 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2019 Guillén-Rogel et al.